There were alternatives to the B-29. The B-32 and even the B-36 (which first flew in 1946). Also the XB-30 and XB-31 were contenders.
The B-32 was intended as a fallback in case of any design or production difficulties with the B-29. In addition, the B-32 was riddled with flaws, like the pressurization system problems that were never solved and eliminated from production models. In addition, only 118 were built out of a 1000+ order for the B-32.
Viable alternative? I don't think so and from everything I've read the USAAC thought the same. By the time the first production B-31 was ready, the B-29 had already been in active service in China. As I mentioned, the B-32 was designed as a 'fallback' if the B-29 suffered from design and production delays but it was the B-32 that suffered production delays due to faulty designs. The USAAC then initially planned on using the B-32 to supplement the B-29 by replacing the B-17s and B-24s of the 8th and 15th AFs before redeployment to the PTO. However, this didn't work out so well when only a handful of B-32s were delivered by the end of '44, which by this time full B-29 operation in the CBI/PTO were fully underway.
B-36 a contender? It wasn't deployed during WW2, its development cycle lasted from 1941 to 1946 with the first prototype flying in 1946. The only reason the USAAF didn't cancell the project is that at the time it was the only bomber capable of carrying a thermonuclear device to the Soviet Union. It also suffered through engine problems its entire production life.
B-31 never made it out of the design stage because Boeing had a huge head start with the B-29 program and it was felt that the B-29 could do everything the B-31 could do and more.
B-30? Same reasons as the B-31.
Was the B-29 perfect? No, but it was the right plane for the right job at the time.
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